Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4_0/mira4.py @ 39:bbf14bb9607b draft default tip

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
author peterjc
date Mon, 03 Jun 2019 13:29:00 -0400
parents cee8f9005e43
children
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38:cee8f9005e43 39:bbf14bb9607b
22 """Run MIRA to find its version number.""" 22 """Run MIRA to find its version number."""
23 # At the commend line I would use: mira -v | head -n 1 23 # At the commend line I would use: mira -v | head -n 1
24 # however there is some pipe error when doing that here. 24 # however there is some pipe error when doing that here.
25 cmd = [mira_binary, "-v"] 25 cmd = [mira_binary, "-v"]
26 try: 26 try:
27 child = subprocess.Popen(cmd, universal_newlines=True, 27 child = subprocess.Popen(
28 stdout=subprocess.PIPE, 28 cmd,
29 stderr=subprocess.STDOUT) 29 universal_newlines=True,
30 stdout=subprocess.PIPE,
31 stderr=subprocess.STDOUT,
32 )
30 except Exception as err: 33 except Exception as err:
31 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) 34 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
32 sys.exit(1) 35 sys.exit(1)
33 ver, tmp = child.communicate() 36 ver, tmp = child.communicate()
34 del child 37 del child
35 return ver.split("\n", 1)[0].strip() 38 return ver.split("\n", 1)[0].strip()
36 39
37 40
38 # Parse Command Line 41 # Parse Command Line
39 usage = """Galaxy MIRA4 wrapper script v%s - use as follows: 42 usage = (
43 """Galaxy MIRA4 wrapper script v%s - use as follows:
40 44
41 $ python mira4.py ... 45 $ python mira4.py ...
42 46
43 This will run the MIRA binary and collect its output files as directed. 47 This will run the MIRA binary and collect its output files as directed.
44 """ % WRAPPER_VER 48 """
49 % WRAPPER_VER
50 )
45 parser = OptionParser(usage=usage) 51 parser = OptionParser(usage=usage)
46 parser.add_option("-m", "--manifest", dest="manifest", 52 parser.add_option(
47 default=None, metavar="FILE", 53 "-m",
48 help="MIRA manifest filename") 54 "--manifest",
49 parser.add_option("--maf", dest="maf", 55 dest="manifest",
50 default="-", metavar="FILE", 56 default=None,
51 help="MIRA MAF output filename") 57 metavar="FILE",
52 parser.add_option("--bam", dest="bam", 58 help="MIRA manifest filename",
53 default="-", metavar="FILE", 59 )
54 help="Unpadded BAM output filename") 60 parser.add_option(
55 parser.add_option("--fasta", dest="fasta", 61 "--maf", dest="maf", default="-", metavar="FILE", help="MIRA MAF output filename"
56 default="-", metavar="FILE", 62 )
57 help="Unpadded FASTA output filename") 63 parser.add_option(
58 parser.add_option("--log", dest="log", 64 "--bam",
59 default="-", metavar="FILE", 65 dest="bam",
60 help="MIRA logging output filename") 66 default="-",
61 parser.add_option("-v", "--version", dest="version", 67 metavar="FILE",
62 default=False, action="store_true", 68 help="Unpadded BAM output filename",
63 help="Show version and quit") 69 )
70 parser.add_option(
71 "--fasta",
72 dest="fasta",
73 default="-",
74 metavar="FILE",
75 help="Unpadded FASTA output filename",
76 )
77 parser.add_option(
78 "--log",
79 dest="log",
80 default="-",
81 metavar="FILE",
82 help="MIRA logging output filename",
83 )
84 parser.add_option(
85 "-v",
86 "--version",
87 dest="version",
88 default=False,
89 action="store_true",
90 help="Show version and quit",
91 )
64 options, args = parser.parse_args() 92 options, args = parser.parse_args()
65 manifest = options.manifest 93 manifest = options.manifest
66 out_maf = options.maf 94 out_maf = options.maf
67 out_bam = options.bam 95 out_bam = options.bam
68 out_fasta = options.fasta 96 out_fasta = options.fasta
70 98
71 if "MIRA4" in os.environ: 99 if "MIRA4" in os.environ:
72 mira_path = os.environ["MIRA4"] 100 mira_path = os.environ["MIRA4"]
73 mira_binary = os.path.join(mira_path, "mira") 101 mira_binary = os.path.join(mira_path, "mira")
74 if not os.path.isfile(mira_binary): 102 if not os.path.isfile(mira_binary):
75 sys.exit("Missing mira under $MIRA4, %r\nFolder contained: %s" 103 sys.exit(
76 % (mira_binary, ", ".join(os.listdir(mira_path)))) 104 "Missing mira under $MIRA4, %r\nFolder contained: %s"
105 % (mira_binary, ", ".join(os.listdir(mira_path)))
106 )
77 mira_convert = os.path.join(mira_path, "miraconvert") 107 mira_convert = os.path.join(mira_path, "miraconvert")
78 if not os.path.isfile(mira_convert): 108 if not os.path.isfile(mira_convert):
79 sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s" 109 sys.exit(
80 % (mira_convert, ", ".join(os.listdir(mira_path)))) 110 "Missing miraconvert under $MIRA4, %r\nFolder contained: %s"
111 % (mira_convert, ", ".join(os.listdir(mira_path)))
112 )
81 else: 113 else:
82 sys.stderr.write("DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n") 114 sys.stderr.write(
115 "DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n"
116 )
83 mira_path = None 117 mira_path = None
84 mira_binary = "mira" 118 mira_binary = "mira"
85 mira_convert = "miraconvert" 119 mira_convert = "miraconvert"
86 120
87 mira_ver = get_version(mira_binary) 121 mira_ver = get_version(mira_binary)
176 if not os.path.isfile(old_fasta): 210 if not os.path.isfile(old_fasta):
177 old_fasta = "%s/%s_out_ReferenceStrain.unpadded.fasta" % (f, name) 211 old_fasta = "%s/%s_out_ReferenceStrain.unpadded.fasta" % (f, name)
178 ref_fasta = "%s/%s_out_ReferenceStrain.padded.fasta" % (f, name) 212 ref_fasta = "%s/%s_out_ReferenceStrain.padded.fasta" % (f, name)
179 213
180 missing = False 214 missing = False
181 for old, new in [(old_maf, out_maf), 215 for old, new in [(old_maf, out_maf), (old_fasta, out_fasta)]:
182 (old_fasta, out_fasta)]:
183 if not os.path.isfile(old): 216 if not os.path.isfile(old):
184 missing = True 217 missing = True
185 elif not new or new == "-": 218 elif not new or new == "-":
186 handle.write("Ignoring %s\n" % old) 219 handle.write("Ignoring %s\n" % old)
187 else: 220 else:
243 276
244 if out_log and out_log != "-": 277 if out_log and out_log != "-":
245 handle = open(out_log, "w") 278 handle = open(out_log, "w")
246 else: 279 else:
247 handle = open(os.devnull, "w") 280 handle = open(os.devnull, "w")
248 handle.write("======================== MIRA manifest (instructions) ========================\n") 281 handle.write(
282 "======================== MIRA manifest (instructions) ========================\n"
283 )
249 m = open(manifest, "rU") 284 m = open(manifest, "rU")
250 for line in m: 285 for line in m:
251 handle.write(line) 286 handle.write(line)
252 m.close() 287 m.close()
253 del m 288 del m
254 handle.write("\n") 289 handle.write("\n")
255 handle.write("============================ Starting MIRA now ===============================\n") 290 handle.write(
291 "============================ Starting MIRA now ===============================\n"
292 )
256 handle.flush() 293 handle.flush()
257 try: 294 try:
258 # Run MIRA 295 # Run MIRA
259 child = subprocess.Popen(cmd_list, 296 child = subprocess.Popen(cmd_list, stdout=handle, stderr=subprocess.STDOUT)
260 stdout=handle,
261 stderr=subprocess.STDOUT)
262 except Exception as err: 297 except Exception as err:
263 log_manifest(manifest) 298 log_manifest(manifest)
264 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) 299 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
265 # TODO - call clean up? 300 # TODO - call clean up?
266 handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) 301 handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
270 stdout, stderr = child.communicate() 305 stdout, stderr = child.communicate()
271 assert not stdout and not stderr # Should be empty as sent to handle 306 assert not stdout and not stderr # Should be empty as sent to handle
272 run_time = time.time() - start_time 307 run_time = time.time() - start_time
273 return_code = child.returncode 308 return_code = child.returncode
274 handle.write("\n") 309 handle.write("\n")
275 handle.write("============================ MIRA has finished ===============================\n") 310 handle.write(
311 "============================ MIRA has finished ===============================\n"
312 )
276 handle.write("MIRA took %0.2f hours\n" % (run_time / 3600.0)) 313 handle.write("MIRA took %0.2f hours\n" % (run_time / 3600.0))
277 if return_code: 314 if return_code:
278 print("MIRA took %0.2f hours" % (run_time / 3600.0)) 315 print("MIRA took %0.2f hours" % (run_time / 3600.0))
279 handle.write("Return error code %i from command:\n" % return_code) 316 handle.write("Return error code %i from command:\n" % return_code)
280 handle.write(cmd + "\n") 317 handle.write(cmd + "\n")
286 sys.exit(return_code) 323 sys.exit(return_code)
287 handle.flush() 324 handle.flush()
288 325
289 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"): 326 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
290 handle.write("\n") 327 handle.write("\n")
291 handle.write("====================== Extract Large Contigs failed ==========================\n") 328 handle.write(
329 "====================== Extract Large Contigs failed ==========================\n" # noqa: E501
330 )
292 e = open("MIRA_assembly/MIRA_d_results/ec.log", "rU") 331 e = open("MIRA_assembly/MIRA_d_results/ec.log", "rU")
293 for line in e: 332 for line in e:
294 handle.write(line) 333 handle.write(line)
295 e.close() 334 e.close()
296 handle.write("============================ (end of ec.log) =================================\n") 335 handle.write(
336 "============================ (end of ec.log) =================================\n" # noqa: E501
337 )
297 handle.flush() 338 handle.flush()
298 339
299 # print("Collecting output...") 340 # print("Collecting output...")
300 start_time = time.time() 341 start_time = time.time()
301 collect_output(temp, name, handle) 342 collect_output(temp, name, handle)
302 collect_time = time.time() - start_time 343 collect_time = time.time() - start_time
303 handle.write("MIRA took %0.2f hours; collecting output %0.2f minutes\n" 344 handle.write(
304 % (run_time / 3600.0, collect_time / 60.0)) 345 "MIRA took %0.2f hours; collecting output %0.2f minutes\n"
305 print("MIRA took %0.2f hours; collecting output %0.2f minutes\n" 346 % (run_time / 3600.0, collect_time / 60.0)
306 % (run_time / 3600.0, collect_time / 60.0)) 347 )
348 print(
349 "MIRA took %0.2f hours; collecting output %0.2f minutes\n"
350 % (run_time / 3600.0, collect_time / 60.0)
351 )
307 352
308 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"): 353 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
309 # Treat as an error, but doing this AFTER collect_output 354 # Treat as an error, but doing this AFTER collect_output
310 sys.stderr.write("Extract Large Contigs failed\n") 355 sys.stderr.write("Extract Large Contigs failed\n")
311 handle.write("Extract Large Contigs failed\n") 356 handle.write("Extract Large Contigs failed\n")